*
* - getVisibleColsIterator: iterates over the visible *columns*
*
- * For performance reasons, provide bounds where possible.
+ * For performance reasons, provide bounds where possible. Note that column
+ * numbering begins at 0 throughout this class.
*
* @author kmourao
*
* list of hidden column [start, end] ranges; the list is maintained in
* ascending start column order
*/
- private ArrayList<int[]> hiddenColumns;
+ private List<int[]> hiddenColumns;
/**
* Constructor
*/
public HiddenColumns(HiddenColumns copy)
{
- try
- {
- LOCK.writeLock().lock();
- numColumns = 0;
- if (copy != null)
- {
- if (copy.hiddenColumns != null)
- {
- hiddenColumns = new ArrayList<>();
- Iterator<int[]> it = copy.iterator();
- while (it.hasNext())
- {
- int[] region = it.next();
- hiddenColumns.add(region);
- numColumns += region[1] - region[0] + 1;
- }
- cursor.resetCursor(hiddenColumns);
- }
- }
- } finally
- {
- LOCK.writeLock().unlock();
- }
+ this(copy, Integer.MIN_VALUE, Integer.MAX_VALUE, 0);
}
/**
* mark the columns corresponding to gap characters as hidden in the column
* selection
*
- * @param sr
+ * @param insertions
*/
- public void hideInsertionsFor(SequenceI sr)
+ public void hideInsertionsFor(List<int[]> inserts)
{
try
{
LOCK.writeLock().lock();
- List<int[]> inserts = sr.getInsertions();
for (int[] r : inserts)
{
hideColumns(r[0], r[1]);
markHiddenRegions(hidden);
hidden.andNot(gaps);
hiddenColumns = null;
- this.hideMarkedBits(hidden);
+ this.hideColumns(hidden);
// for each sequence in the alignment, except the profile sequence,
// insert gaps corresponding to each hidden region but where each hidden
// column region is shifted backwards by the number of preceding visible
// gaps update hidden columns at the same time
Iterator<int[]> regions = hiddenColumns.iterator();
- ArrayList<int[]> newhidden = new ArrayList<>();
+ List<int[]> newhidden = new ArrayList<>();
int numGapsBefore = 0;
int gapPosition = 0;
* int column index in alignment view (count from zero)
* @return alignment column index for column
*/
- public int adjustForHiddenColumns(int column)
+ public int visibleToAbsoluteColumn(int column)
{
try
{
if (hiddenColumns != null)
{
- result += cursor.getHiddenOffset(column).getHiddenSoFar();
+ result += cursor.findRegionForVisColumn(column).getHiddenSoFar();
}
return result;
/**
* Use this method to find out where a column will appear in the visible
* alignment when hidden columns exist. If the column is not visible, then the
- * left-most visible column will always be returned.
+ * index of the next visible column on the left will be returned (or 0 if
+ * there is no visible column on the left)
*
* @param hiddenColumn
* the column index in the full alignment including hidden columns
* @return the position of the column in the visible alignment
*/
- public int findColumnPosition(int hiddenColumn)
+ public int absoluteToVisibleColumn(int hiddenColumn)
{
try
{
int distance = visibleDistance;
// in case startColumn is in a hidden region, move it to the left
- int start = adjustForHiddenColumns(findColumnPosition(startColumn));
+ int start = visibleToAbsoluteColumn(absoluteToVisibleColumn(startColumn));
Iterator<int[]> it = new ReverseRegionsIterator(0, start,
hiddenColumns);
* @param alPos
* the absolute (visible) alignmentPosition to find the next hidden
* column for
+ * @return the index of the next hidden column, or alPos if there is no next
+ * hidden column
*/
public int getHiddenBoundaryRight(int alPos)
{
if (foundStart)
{
- return findColumnPosition(start);
+ return absoluteToVisibleColumn(start);
}
// otherwise, sequence was completely hidden
return visPrev;
try
{
LOCK.readLock().lock();
+
+ // we don't use getSize()>0 here because it has to iterate over
+ // the full hiddenColumns collection and so will be much slower
return hiddenColumns != null && hiddenColumns.size() > 0;
} finally
{
/**
*
- * @return true if there are more than one set of columns hidden
+ * @return true if there is more than one hidden column region
*/
- public boolean hasManyHiddenColumns()
+ public boolean hasMultiHiddenColumnRegions()
{
try
{
* @param inserts
* - columns map to bits starting from zero
*/
- public void hideMarkedBits(BitSet inserts)
+ public void hideColumns(BitSet inserts)
{
try
{
*
* @param res
* visible residue position, unadjusted for hidden columns
- * @return region as [start,end] or null if no matching region is found
+ * @return region as [start,end] or null if no matching region is found. If
+ * res is adjacent to two regions, returns the left region.
*/
public int[] getRegionWithEdgeAtRes(int res)
{
try
{
LOCK.readLock().lock();
- int adjres = adjustForHiddenColumns(res);
+ int adjres = visibleToAbsoluteColumn(res);
int[] reveal = null;
try
{
LOCK.readLock().lock();
- return new BoundedHiddenColsIterator(hiddenColumns);
+ return new HiddenColsIterator(hiddenColumns);
} finally
{
LOCK.readLock().unlock();
try
{
LOCK.readLock().lock();
- return new BoundedHiddenColsIterator(start, end, hiddenColumns);
+ return new HiddenColsIterator(start, end, hiddenColumns);
} finally
{
LOCK.readLock().unlock();
LOCK.readLock().lock();
// get absolute position of column in alignment
- int absoluteStart = adjustForHiddenColumns(start);
+ int absoluteStart = visibleToAbsoluteColumn(start);
// Get cursor position and supply it to the iterator:
// Since we want visible region start, we look for a cursor for the
int adjend = end;
if (useVisibleCoords)
{
- adjstart = adjustForHiddenColumns(start);
- adjend = adjustForHiddenColumns(end);
+ adjstart = visibleToAbsoluteColumn(start);
+ adjend = visibleToAbsoluteColumn(end);
}
try
git://source.jalview.org / jalview.git / blobdiff